Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 14:2fe07f50a41e draft
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
author | peterjc |
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date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 623f727cdff1 |
children | c16c30e9ad5b |
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Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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1 <tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.01"> |
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2 <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> |
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3 <description>masks low complexity regions</description> |
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4 <macros> |
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5 <token name="@BINARY@">dustmasker</token> |
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6 <import>ncbi_macros.xml</import> |
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7 </macros> |
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8 <expand macro="requirements" /> |
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9 <command> |
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10 ## The command is a Cheetah template which allows some Python based syntax. |
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11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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12 dustmasker |
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13 #if $db_opts.db_opts_selector == "db": |
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14 -in "${db_opts.database.fields.path}" -infmt blastdb |
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15 #elif $db_opts.db_opts_selector == "histdb": |
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16 -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb |
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17 #else: |
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18 -in "$subject" -infmt fasta |
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19 #end if |
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20 -out "$outfile" |
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21 -window $window -level $level -linker $linker -outfmt $outformat |
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22 </command> |
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23 <expand macro="stdio" /> |
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24 <inputs> |
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25 <expand macro="input_conditional_nucleotide_db" /> |
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26 <param name="window" type="integer" value="64" label="DUST window length" /> |
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27 <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> |
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28 <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> |
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29 <param name="outformat" type="select" label="Output format"> |
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30 <!-- seqloc_* formats are not very useful |
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31 and what BLAST+ calls 'interval' is not what Galaxy calls interval format |
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32 --> |
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33 <option value="fasta">FASTA</option> |
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34 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> |
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35 <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option> |
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36 <option value="maskinfo_xml">maskinfo_xml</option> |
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37 </param> |
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38 </inputs> |
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39 <outputs> |
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40 <data name="outfile" format="maskinfo-asn1" label="DUST Masked File"> |
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41 <change_format> |
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42 <when input="outformat" value="fasta" format="fasta" /> |
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43 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> |
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44 <!-- |
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45 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> |
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46 --> |
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47 <when input="outformat" value="maskinfo_xml" format="xml" /> |
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48 </change_format> |
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49 </data> |
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50 </outputs> |
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51 <tests> |
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52 <test> |
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53 <param name="db_opts_selector" value="file" /> |
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54 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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55 <param name="window" value="64" /> |
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56 <param name="level" value="20" /> |
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57 <param name="linker" value="1" /> |
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58 <param name="outformat" value="fasta" /> |
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59 <output name="outfile" file="dustmasker_three_human.fasta" /> |
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60 </test> |
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61 <test> |
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62 <param name="db_opts_selector" value="file" /> |
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63 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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64 <param name="window" value="64" /> |
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65 <param name="level" value="20" /> |
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66 <param name="linker" value="1" /> |
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67 <param name="outformat" value="maskinfo_asn1_bin" /> |
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68 <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> |
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69 </test> |
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70 <test> |
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71 <param name="db_opts_selector" value="file" /> |
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72 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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73 <param name="window" value="64" /> |
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74 <param name="level" value="20" /> |
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75 <param name="linker" value="1" /> |
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76 <param name="outformat" value="maskinfo_asn1_text" /> |
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77 <output name="outfile" file="dustmasker_three_human.maskinfo-asn1" /> |
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78 </test> |
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79 </tests> |
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80 <help> |
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81 **What it does** |
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82 |
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83 This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST_ algorithm. |
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84 |
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85 If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. |
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86 |
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87 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. |
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88 |
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89 .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ |
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90 .. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 |
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91 |
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92 **References** |
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93 |
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94 If you use this Galaxy tool in work leading to a scientific publication please |
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95 cite the following papers (a more specific paper covering this wrapper is planned): |
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96 |
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97 @REFERENCES@ |
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98 </help> |
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Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
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99 <expand macro="blast_citations" /> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
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100 </tool> |